Police said the three charges would be prosecuted as a hate crime. The Hindu temple was destroyed in the arson.
The three men accused are Christopher Pollard, 33, Scott Ryan, 33, and Damien Marsh, 34, all from Hamilton. They are charged with arson, possession of incendiary materials and mischief under $5,000.
Police said the three are scheduled to appear in court Wednesday.
"In 2013, Hamilton police service received new information from the public," said Sgt. Matt Kavanagh of Hamilton Police. "The accused parties have been linked to both crime scenes." Police would not say what new information had been gathered to lead to the arrests.
The attack on the temple took place in the early morning of Sept. 15, 2001 while the Hamilton mosque was also targeted by vandalism. The incidents received international attention in the days following.
Hamilton Mayor Bob Bratina spoke about the attention the incidents received. He said "this went around the world that Hamilton, Ontario had suffered this terrible occurrence. If you ever felt you were not fully integrated into the fabric of Hamilton, you are now more than most of us."
Flames erupted around 5:30 a.m. at the temple, which was destroyed. Members of Hamilton's Muslim community expressed shock and sadness over the fire. There were several reports of death threats and vandalism against Muslims in Canada after terrorists hijacked four planes and killed thousands of people in the United States Sept. 11.
Police said the three arrests were made Tuesday. Investigators believe there are more people who have knowledge of the arson, and want them to contact police.